LOCUS JAIFWH010000056 4213 bp DNA linear ENV 17-AUG-2021 DEFINITION MAG: Candidatus Parcubacteria bacterium isolate viral-cat_42_19 PAFVLPS_2018_scaffold_124033, whole genome shotgun sequence. ACCESSION JAIFWH010000056 JAIFWH010000000 VERSION JAIFWH010000056.1 DBLINK BioProject: PRJNA744897 BioSample: SAMN20125907 KEYWORDS WGS; Metagenome Assembled Genome; MAG. SOURCE Candidatus Parcubacteria bacterium (rhizosphere metagenome) ORGANISM Candidatus Parcubacteria bacterium Bacteria; Candidatus Parcubacteria. REFERENCE 1 (bases 1 to 4213) AUTHORS Nicolas,A.M., Jaffe,A.L., Nuccio,E., Taga,M.E., Firestone,M.K. and Banfield,J.F. TITLE Soil Candidate Phyla Radiation bacteria encode components of aerobic metabolism and co-occur with nanoarchaea in the rare biosphere of rhizosphere grassland communities JOURNAL Unpublished REFERENCE 2 (bases 1 to 4213) AUTHORS Nicolas,A.M., Jaffe,A.L., Nuccio,E., Taga,M.E., Firestone,M.K. and Banfield,J.F. TITLE Direct Submission JOURNAL Submitted (08-JUL-2021) Plant & Microbial Biology, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, USA COMMENT The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Assembly-Data-START## Assembly Date :: 11-JUN-2019 Assembly Method :: IDBA_UD v. June-2019 Genome Representation :: Full Expected Final Version :: Yes Genome Coverage :: 19.14x Sequencing Technology :: Illumina HiSeq ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/12/2021 15:29:28 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method :: Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision :: 5.2 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total) :: 871 CDSs (total) :: 837 Genes (coding) :: 831 CDSs (with protein) :: 831 Genes (RNA) :: 34 rRNAs :: 1 (23S) partial rRNAs :: 1 (23S) tRNAs :: 33 ncRNAs :: 0 Pseudo Genes (total) :: 6 CDSs (without protein) :: 6 Pseudo Genes (ambiguous residues) :: 0 of 6 Pseudo Genes (frameshifted) :: 2 of 6 Pseudo Genes (incomplete) :: 4 of 6 Pseudo Genes (internal stop) :: 0 of 6 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..4213 /organism="Candidatus Parcubacteria bacterium" /mol_type="genomic DNA" /submitter_seqid="PAFVLPS_2018_scaffold_124033" /isolate="viral-cat_42_19" /isolation_source="0.2 micron size-filtered soil effluent from rhizosphere-associated grassland soil" /db_xref="taxon:2762014" /environmental_sample /geo_loc_name="USA: Hopland, California" /lat_lon="39.004160 N 123.086009 W" /collection_date="2018-02-16" /metagenome_source="rhizosphere metagenome" /note="metagenomic" gene 142..489 /locus_tag="KW783_02890" CDS 142..489 /locus_tag="KW783_02890" /inference="COORDINATES: ab initio prediction:GeneMarkS-2+" /note="Derived by automated computational analysis using gene prediction method: GeneMarkS-2+." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="MBX4210891.1" /translation="MGLNKLERSLQMRKTHLDAKKQVPKEVIKKVESEKDMIKAAKYI LRQDTIKACAILDMLWGVQSAILLGVFISVFRKNVRSKKLLRRARYLKIRGTKGLGYE RNKYYRETGCLLI" gene 570..1028 /locus_tag="KW783_02895" CDS 570..1028 /locus_tag="KW783_02895" /inference="COORDINATES: similar to AA sequence:RefSeq:WP_018615180.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="NUDIX domain-containing protein" /protein_id="MBX4210892.1" /translation="MKKVSAGLLMFRKKNSILEFLLVHPGGPLFKNKDDGFWTIPKGI VEDGEDPLKAAQREFEEETSIKVSPDATLIPLGTIEQTNNKTVWGWAFQGNADATKIK SNTFDVEWPPKSGKKITIPEIDRGEFFDYETAVKKINPDQIPFLDVINNL" gene 1096..1620 /locus_tag="KW783_02900" CDS 1096..1620 /locus_tag="KW783_02900" /inference="COORDINATES: ab initio prediction:GeneMarkS-2+" /note="Derived by automated computational analysis using gene prediction method: GeneMarkS-2+." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="MBX4210893.1" /translation="MLWIGILIGIVVGTVFTFTLRRANLFPDTGHRVYGMKDVFALAL LLEALKEVTGLRKKMDIDSGPTHQRLLSDGHSVLAYFDDAIGELPRNAMSIVVKNPEV AAFRVYQILNDNDFKAEMHKPLPGLEKEFVMVTSVAFSGWGLAFRRAWPVMAWREHQV GKRKRAEVERLARL" gene 1685..2824 /locus_tag="KW783_02905" CDS 1685..2824 /locus_tag="KW783_02905" /inference="COORDINATES: protein motif:HMM:NF013012.2,HMM:TIGR00329.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD" /protein_id="MBX4210894.1" /translation="MKILAIETSCDETAISIIEASGAVLKPEFKVLGNAVLSQIIHKE YGGVYPNLAKREHEKNLIPIFEKVLKEAKLFTKSMHDIDNEALEKILVKEPELFKHFI EFIGTIDKPDIDYIAVTSGPGLEPALWVGIKFAEALSHVWNISVLPINHMEGHIASVL YKNTAAIEFPALALLISGGHTELVLAKKWGKYEILGQTRDDAVGEAFDKVARLLGLPY PGGPEISKLAAIAREKNLPRQFELPRPMIKSDDFDFSFSGIKTAVLYTLKKIGDVTQE IREDMSREFEDAVTEVLIAKTEKALETHAAKSLILGGGVIANTHIRSEFEKLILNYPD VRLNLPAKEITTDNALMIALAAFVHLSKGEEISTSQISAEGNLKL" gene complement(2825..>4213) /locus_tag="KW783_02910" CDS complement(2825..>4213) /locus_tag="KW783_02910" /inference="COORDINATES: ab initio prediction:GeneMarkS-2+" /note="Derived by automated computational analysis using gene prediction method: GeneMarkS-2+." /codon_start=1 /transl_table=11 /product="peptidoglycan-binding protein" /protein_id="MBX4210895.1" /translation="PTNPGGDQVTAVFDTGCGTTTTAILTITTDNPNNGGGGGGGGSG GGGGGGGGGGGGSYQLRIFNERVAEVPAGVAFVQWDTNLVASTRVVFGTTSVATITSG PNFGYATSTFELTERVTAHSMALFGLSEGVTYYMRPVSSDGVTTAVGRELSFRIGTPQ SGGTGGGPETCLYLRDFLKISFNNDPAEVRKLQIFLRDLEGHANLQVTGVFDVATFNA VSAFQKKYANDILTPWGYEPSQPTGFVYILTRKKINEIYCNQAFPLTAVQQQEIAAFR AFLESLKRAGITPPSGYDGGTVGLGHNNGGTTSTSTVGTSTNDGIIIDNNIVGEENSG SILGNAYLRNLAAAAVTLPKSWQDATKCLLVLLLMLGIIYSAYFVWGTDEENTQKTQT GRLAFYTVGIILAIILSIVFKQYCEIIPLLIILVILIISLIANAPRRKTIQLPPAKPP ITTIMPRDNTPE" BASE COUNT 1249 a 889 c 922 g 1153 t ORIGIN 1 acgacacgct ctaccaactg agctaaccgc ccaatactgt atcaagatat cttagtttat 61 tcagttcgca atgtcatttg acaatcttca tttactttgc ataatcagtt tagaaacaca 121 ttctacaaac aaggaggccc tgtgggtctg aataagcttg aacgatcgtt gcagatgcga 181 aaaacgcatt tggacgcaaa aaaacaggtt ccaaaagagg tcattaaaaa agtcgagtcg 241 gaaaaagaca tgattaaagc cgcgaagtat atactgcggc aggatacgat taaggcgtgt 301 gcgatcctcg acatgttgtg gggcgtgcaa tcagcaatct tgctcggtgt ttttatttcg 361 gtatttagaa aaaacgtgcg atcaaaaaaa ctcttgagac gtgcacgata tctcaaaatt 421 cggggcacaa agggactggg gtacgaacga aacaagtatt accgtgaaac tggctgtctc 481 ctgatctaat gcaatttcca gttcatagtt tagccgcatc tcaatgattc ggcttttttt 541 attggcgtat aaatgccata atgccattta tgaaaaaagt aagtgcagga cttttaatgt 601 tcaggaaaaa aaacagcata ttagagtttt tacttgtgca cccaggcgga ccacttttta 661 aaaataaaga tgatggattt tggactattc caaaaggtat tgtagaagac ggcgaagacc 721 ctttgaaagc cgctcaaaga gaatttgaag aagaaacaag tattaaagtt tctcctgacg 781 caacattaat tcccctcgga acaattgaac agacaaataa taagacagta tggggttggg 841 cgtttcaagg taacgctgat gcaaccaaaa ttaaaagcaa tacattcgat gtcgaatggc 901 cgccaaaaag tggaaagaag ataacgattc ctgaaattga tcgcggcgaa ttttttgact 961 acgaaactgc tgttaaaaaa ataaatcctg accaaattcc ctttttggat gtgataaaca 1021 atctataact cttgcttttt tttaaattct cagtatagtt ttgccagaat caaactcttg 1081 aaaggagtgt gttcaatgct atggataggt attcttatcg ggatcgtggt tggtactgtg 1141 ttcaccttta ctttacgaag ggcaaatctt tttcctgata ctggtcaccg tgtctatgga 1201 atgaaggatg tcttcgcgtt ggcccttctg ctggaagccc tcaaagaggt caccgggctt 1261 cgaaagaaaa tggatattga tagcggcccg acgcatcaac ggcttctgtc cgacggacat 1321 tcggtccttg cctacttcga tgatgcaatc ggtgaactgc cacgcaatgc catgtctatc 1381 gtcgtaaaaa acccagaagt cgcagcgttt agagtttatc aaattttaaa tgataacgac 1441 ttcaaggcag agatgcataa gccgttacca ggactggaaa aagaatttgt catggtaaca 1501 tcagtcgcat tctcgggctg gggtctagca ttcagacgtg cgtggccagt catggcctgg 1561 agagaacatc aggttggaaa gagaaaaagg gctgaagtgg agcggttggc tcgcctgtga 1621 caattgaaga tgatgaccgc agatgtatcg cggtcatttt tatttatgtt agtatcaatg 1681 cgttatgaaa atattagcca tcgagacaag ctgtgatgaa acagcaataa gcataatcga 1741 ggcaagtggc gcagttttga aacctgaatt taaagttttg ggcaatgctg ttctgtcaca 1801 aattattcat aaagaatacg gcggcgtata tcccaatctt gctaaacgcg aacatgagaa 1861 aaatctcatt ccaatttttg aaaaagttct taaagaagcc aaacttttta ccaagtctat 1921 gcacgatata gataatgaag cgctcgaaaa aatactagtc aaagagccgg aactttttaa 1981 acattttatt gaatttatcg gaactataga taaacctgat attgattata ttgccgtaac 2041 ttctgggccg ggacttgagc ctgctctgtg ggtcggaatt aaatttgcgg aggcactttc 2101 gcacgtgtgg aacatttctg tattgcctat aaatcacatg gaaggtcaca ttgcttcagt 2161 tttatacaaa aatacagcag ctatagaatt ccctgcctta gccttgctta tttccggcgg 2221 ccacactgag ttggttttgg caaagaaatg gggcaaatat gaaatacttg gacaaacacg 2281 agacgacgcc gtcggtgaag catttgataa agtcgcgcgg ctactcggac ttccctatcc 2341 tggcggaccg gagatttcaa aattagcagc aattgctcgg gagaagaatc tgccgcggca 2401 attcgaattg ccgcggccaa tgattaagtc cgacgacttc gacttttctt tttcgggcat 2461 taaaacagca gtactttata cgctgaaaaa aatcggagat gtgacacaag aaatccgcga 2521 agatatgtcg cgagaattcg aagatgctgt tactgaagtg cttatcgcaa aaacagaaaa 2581 agcactcgaa actcacgccg caaaaagtct tattctcggt ggcggagtta ttgcaaatac 2641 ccacatccgt tcagaatttg aaaaacttat tttaaactac cccgatgtta gactgaatct 2701 accggcaaag gaaatcacga cagacaatgc gctcatgatt gcgcttgccg cttttgtaca 2761 cctttccaaa ggagaagaaa tctcaacgtc acaaatctct gcagaaggaa atcttaaact 2821 ctaattactc cggtgtattg tcccgcggca taattgtcgt aatcggcggc tttgcaggtg 2881 gcagctgtat tgtttttctc cgcggagcat tcgcaataag agaaataata agtatgacaa 2941 ggattataag aagcggaata atttcacagt attgtttaaa gacaatcgat aagattatcg 3001 caagtataat tcccaccgtg tagaaagcca gacggcctgt ttgtgtcttt tgcgtattct 3061 cttcgtcagt tccccagaca aagtaagcac tgtagattat gccgagcatg agaagcaaaa 3121 ctaaaagaca ttttgtcgca tcttgccagc tttttggcag tgttaccgca gccgctgcaa 3181 ggtttcgaag atacgcattt ccgagaattg aaccggaatt ttcttctcca acaatattgt 3241 tatctataat aatcccatcg tttgtacttg ttccgactgt cgatgtggat gtcgtaccgc 3301 cattattatg accaagccca actgtacctc cgtcatatcc agatggagga gtaatacctg 3361 cacgcttgag actttcgaga aatgctctga aggcggcaat ttcctgttgc tgtactgctg 3421 ttaatggaaa agcttgatta caataaattt cgttaatttt tttacgagtc aggatataaa 3481 caaagcctgt tggttgcgat ggctcatatc cccacggagt taaaatgtcg ttcgcatatt 3541 tcttttggaa agctgacaca gcgttaaatg tggcgacatc aaagacaccg gttacttgga 3601 gattggcatg tccctctaga tctcgcaaga agatctggag tttacgcact tctgcgggat 3661 cattattaaa cgaaattttc aaaaagtcgc gaagatacaa acatgtttca ggacctccgc 3721 ctgtgccgcc tgactgcggt gtaccgattc taaaggacaa ttctcgtcca actgccgtcg 3781 taactccatc ggaagaaact ggtctcatgt aataggttac tccctctgaa agtccgaata 3841 gtgccattga gtgagcggtt acgcgttcgg tcagttcaaa tgtacttgtt gcgtatccaa 3901 aatttggacc gcttgtgatc gtcgcaacac ttgttgttcc aaacacaacg cgagttgaag 3961 ctacaaggtt tgtgtcccat tgaacaaagg caactccagc aggaacttct gcaactcttt 4021 cgttaaaaat tcggagttga taacttcctc cgccaccacc accgcctcca ccaccgcctc 4081 caccgcttcc gccaccacca ccgccccccc cgttgttcgg attgtcagtt gttatggtca 4141 gaattgcggt cgtcgttgtg ccacagcccg tgtcaaagac agctgtaact tgatctccac 4201 caggatttgt agg //